I just thought I would post for the first time on the Rochester Forum and I must say this is awesome.
Any way. One new (to me) way that I have stared to do when trolling in rough water is to put the trolling motor down at the same time as I run the kicker motor (autopilot workes the best in this situation, but can be done with a longer corded trolling motor). This allows you to control the front end of the boat a lot better in windy and/or rough water. Think of it as four wheel drive for the boat.
With the wind pushing the front around and off track you now have control of the bow at the same time you are able to push the boat with the kicker or big motor. Believe me after taking 3-4ft waves I am very impressed with what I learned.
The key is to steer with the trolling motor and speed control with the kicker. You can play around with the trolling motor speed, But I used just enough to keep on track.
This may not work at faster trolling speeds for trolling motor may not be able to handle it, but it worked up to 2.5 mph for the unit I was working.
So, the next time in a situation like this try trolling at both ends of the boat.
Good Luck
Aaron K.